Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.

Sascha Ott

Syed Sabih Ur Rehman Muhammad Ibtisam Nasar Cristina S. Mesquita Souhaila Al Khodor Richard A. Notebaart Sascha Ott Sunil Mundra Ramesh P. Arasardanam Khalid Muhammad Mohammad Tauqeer Alam Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions. 2025 July 26 Briefings Bioinform. 4 https://doi.org/10.1093/bib/bbaf323 db/journals/bib/bib26.html#RehmanNMKNOMAMA25 streams/journals/bib

Denise Vlachou Maria Veretennikova Laura Usselmann Vadim Vasilyev Sascha Ott Georg A. Bjarnason Robert Dallmann Francis Lévi David A. Rand TimeTeller: A tool to probe the circadian clock as a multigene dynamical system. 2024 February 20 PLoS Comput. Biol. 2 https://doi.org/10.1371/journal.pcbi.1011779 db/journals/ploscb/ploscb20.html#VlachouVUVOBDLR24

Krzysztof Polanski Bo Gao 0001 Sam A. Mason Paul Brown Sascha Ott Katherine J. Denby David L. Wild Bringing numerous methods for expression and promoter analysis to a public cloud computing service. 884-886 2018 34 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btx692 https://www.wikidata.org/entity/Q47612616 db/journals/bioinformatics/bioinformatics34.html#PolanskiGMBODW18

Krzysztof Polanski Johanna Rhodes Claire Hill Peijun Zhang Dafyd J. Jenkins Steven J. Kiddle Aleksey Jironkin Jim Beynon Vicky Buchanan-Wollaston Sascha Ott Katherine J. Denby Wigwams: identifying gene modules co-regulated across multiple biological conditions. 962-970 2014 30 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btt728 https://www.wikidata.org/entity/Q38534062 db/journals/bioinformatics/bioinformatics30.html#PolanskiRHZJKJBBOD14

Paul Brown Laura Baxter Richard Hickman Jim Beynon Jonathan D. Moore Sascha Ott MEME-LaB: motif analysis in clusters. 1696-1697 2013 29 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btt248 https://www.wikidata.org/entity/Q41556168 db/journals/bioinformatics/bioinformatics29.html#BrownBHBMO13

Hashem Koohy Nigel P. Dyer John E. Reid Georgy Koentges Sascha Ott An alignment-free model for comparison of regulatory sequences. 2391-2397 2010 26 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btq453 https://www.wikidata.org/entity/Q48063607 db/journals/bioinformatics/bioinformatics26.html#KoohyDRKO10

John E. Reid Sascha Ott Lorenz Wernisch Transcriptional programs: Modelling higher order structure in transcriptional control. 2009 10 BMC Bioinform. https://doi.org/10.1186/1471-2105-10-218 https://www.wikidata.org/entity/Q33483024 db/journals/bmcbi/bmcbi10.html#ReidOW09

Kenneth Evans Sascha Ott Annika Hansen Georgy Koentges Lorenz Wernisch A comparative study of S/MAR prediction tools. 2007 8 BMC Bioinform. https://doi.org/10.1186/1471-2105-8-71 https://www.wikidata.org/entity/Q33276687 db/journals/bmcbi/bmcbi8.html#EvansOHKW07

Tatsuya Akutsu Hideo Bannai Satoru Miyano Sascha Ott On the complexity of deriving position specific score matrices from positive and negative sequences. 676-685 2007 155 Discret. Appl. Math. 6-7 https://doi.org/10.1016/j.dam.2004.10.011 db/journals/dam/dam155.html#AkutsuBMO07

Sascha Ott Annika Hansen SunYong Kim Satoru Miyano Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution. 227-238 2005 21 Bioinform. 2 https://doi.org/10.1093/bioinformatics/bth484 https://www.wikidata.org/entity/Q48523203 db/journals/bioinformatics/bioinformatics21.html#OttHKM05

Sascha Ott Seiya Imoto Satoru Miyano Finding Optimal Models for Small Gene Networks. 557-567 2004 conf/psb/2004 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb04/ott.pdf db/conf/psb/psb2004.html#OttIM04 Sascha Ott Yoshinori Tamada Hideo Bannai Kenta Nakai Satoru Miyano Intrasplicing - Analysis of Long Intron Sequences. 339-350 2003 conf/psb/2003 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb03/ott.pdf db/conf/psb/psb2003.html#OttTBNM03 Tatsuya Akutsu Sascha Ott Inferring a Union of Halfspaces from Examples. 117-126 2002 conf/cocoon/2002 COCOON https://doi.org/10.1007/3-540-45655-4_14 db/conf/cocoon/cocoon2002.html#AkutsuO02 Tatsuya Akutsu Hideo Bannai Satoru Miyano Sascha Ott On the Complexity of Deriving Position Specific Score Matrices from Examples. 168-177 2002 conf/cpm/2002 CPM https://doi.org/10.1007/3-540-45452-7_15 db/conf/cpm/cpm2002.html#AkutsuBMO02 Sascha Ott Lower Bounds for Approximating Shortest Superstrings over an Alphabet of Size 2. 55-64 https://doi.org/10.1007/3-540-46784-X_7 1999 conf/wg/1999 WG db/conf/wg/wg99.html#Ott99 Tatsuya Akutsu Mohammad Tauqeer Alam Ramesh P. Arasardanam Hideo Bannai Laura Baxter Jim Beynon Georg A. Bjarnason Paul Brown Vicky Buchanan-Wollaston Robert Dallmann Katherine J. Denby Nigel P. Dyer Kenneth Evans Bo Gao 0001 Annika Hansen Richard Hickman Claire Hill Seiya Imoto Dafyd J. Jenkins Aleksey Jironkin Souhaila Al Khodor Steven J. Kiddle SunYong Kim Georgy Koentges Hashem Koohy Francis Lévi Sam A. Mason Cristina S. Mesquita Satoru Miyano Jonathan D. Moore Khalid Muhammad Sunil Mundra Kenta Nakai Muhammad Ibtisam Nasar Richard A. Notebaart Krzysztof Polanski David A. Rand Syed Sabih Ur Rehman John E. Reid Johanna Rhodes Yoshinori Tamada Laura Usselmann Vadim Vasilyev Maria Veretennikova Denise Vlachou Lorenz Wernisch David L. Wild Peijun Zhang